When you do the upper end of an engine you run a small risk of having great compression on top of aworn bottom end. How many miles and was it running good before. If you have been the owner for a long time and know the maintenance has been good if it has life left in it run it till it drops. Take a look at the top of the cylinders while the heads is removed and see how much of a ridge you have if it is less than .005 run it if it is more I would at least run a cylinder hone in their.
As for the reassembly and flushing an engine personally I would do this. Reassemble and just drain theoil before starting. Put in some cheap fresh oil run for a few days or at least more than 100 miles and change oil and filter then put back in you synthetic. Should be good.i
89YJ 2.5L TBI, AX-5, NP231 SYE, Tom Woods Shaft, 33" BFG T/As, 4" lift.
AF Jeep Club Tail #184